[2023-03-19 02:25:43,927] [INFO] DFAST_QC pipeline started.
[2023-03-19 02:25:43,929] [INFO] DFAST_QC version: 0.5.7
[2023-03-19 02:25:43,929] [INFO] DQC Reference Directory: /var/lib/cwl/stg4164167b-b57d-43ff-80b4-39941cdcd0c3/dqc_reference
[2023-03-19 02:25:45,025] [INFO] ===== Start taxonomy check using ANI =====
[2023-03-19 02:25:45,025] [INFO] Task started: Prodigal
[2023-03-19 02:25:45,026] [INFO] Running command: cat /var/lib/cwl/stgfe68610f-8293-4d1a-a088-c1735caac03c/OceanDNA-b14795.fa | prodigal -d OceanDNA-b14795/cds.fna -a OceanDNA-b14795/protein.faa -g 11 -q > /dev/null
[2023-03-19 02:25:51,524] [INFO] Task succeeded: Prodigal
[2023-03-19 02:25:51,524] [INFO] Task started: HMMsearch
[2023-03-19 02:25:51,524] [INFO] Running command: hmmsearch --tblout OceanDNA-b14795/hmmer_result.tsv -E 1E-50 /var/lib/cwl/stg4164167b-b57d-43ff-80b4-39941cdcd0c3/dqc_reference/reference_markers.hmm OceanDNA-b14795/protein.faa > /dev/null
[2023-03-19 02:25:51,706] [INFO] Task succeeded: HMMsearch
[2023-03-19 02:25:51,707] [WARNING] Found 5/6 markers. [/var/lib/cwl/stgfe68610f-8293-4d1a-a088-c1735caac03c/OceanDNA-b14795.fa]
[2023-03-19 02:25:51,734] [INFO] Query marker FASTA was written to OceanDNA-b14795/markers.fasta
[2023-03-19 02:25:51,734] [INFO] Task started: Blastn
[2023-03-19 02:25:51,734] [INFO] Running command: blastn -query OceanDNA-b14795/markers.fasta -db /var/lib/cwl/stg4164167b-b57d-43ff-80b4-39941cdcd0c3/dqc_reference/reference_markers.fasta -out OceanDNA-b14795/blast.markers.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2023-03-19 02:25:52,238] [INFO] Task succeeded: Blastn
[2023-03-19 02:25:52,247] [INFO] Selected 16 target genomes.
[2023-03-19 02:25:52,247] [INFO] Target genome list was writen to OceanDNA-b14795/target_genomes.txt
[2023-03-19 02:25:52,256] [INFO] Task started: fastANI
[2023-03-19 02:25:52,256] [INFO] Running command: fastANI --query /var/lib/cwl/stgfe68610f-8293-4d1a-a088-c1735caac03c/OceanDNA-b14795.fa --refList OceanDNA-b14795/target_genomes.txt --output OceanDNA-b14795/fastani_result.tsv --threads 1
[2023-03-19 02:25:58,199] [INFO] Task succeeded: fastANI
[2023-03-19 02:25:58,199] [INFO] Loading species specific ANI threshold from /var/lib/cwl/stg4164167b-b57d-43ff-80b4-39941cdcd0c3/dqc_reference/prokaryote_ANI_species_specific_threshold.txt
[2023-03-19 02:25:58,199] [WARNING] Species-specific ANI threshold file not found. Will use the default threshold for all species. [/var/lib/cwl/stg4164167b-b57d-43ff-80b4-39941cdcd0c3/dqc_reference/prokaryote_ANI_species_specific_threshold.txt]
[2023-03-19 02:25:58,200] [INFO] Found 0 fastANI hits (0 hits with ANI > threshold)
[2023-03-19 02:25:58,200] [INFO] The taxonomy check result is classified as 'no_hit'.
[2023-03-19 02:25:58,200] [INFO] DFAST Taxonomy check final result
--------------------------------------------------------------------------------
organism_name	strain	accession	taxid	species_taxid	relation_to_type	validated	ani	matched_fragments	total_fragments	ani_threshold	status
--------------------------------------------------------------------------------
[2023-03-19 02:25:58,203] [INFO] DFAST Taxonomy check result was written to OceanDNA-b14795/tc_result.tsv
[2023-03-19 02:25:58,206] [INFO] ===== Taxonomy check completed =====
[2023-03-19 02:25:58,206] [INFO] ===== Start completeness check using CheckM =====
[2023-03-19 02:25:58,206] [INFO] Setting CHECKM_DATA_PATH to /var/lib/cwl/stg4164167b-b57d-43ff-80b4-39941cdcd0c3/dqc_reference/checkm_data
[2023-03-19 02:25:58,259] [INFO] Selected 'Prokaryote' markers (life, taxid=0) for CheckM
[2023-03-19 02:25:58,264] [INFO] Task started: CheckM
[2023-03-19 02:25:58,264] [INFO] Running command: checkm taxonomy_wf --tab_table -f OceanDNA-b14795/cc_result.tsv -t 1 life "Prokaryote" OceanDNA-b14795/checkm_input OceanDNA-b14795/checkm_result
[2023-03-19 02:26:21,110] [INFO] Task succeeded: CheckM
[2023-03-19 02:26:21,110] [INFO] Completeness check finished.
--------------------------------------------------------------------------------
Completeness: 81.02%
Contamintation: 0.00%
Strain heterogeneity: 0.00%
--------------------------------------------------------------------------------
[2023-03-19 02:26:21,143] [INFO] ===== Completeness check finished =====
[2023-03-19 02:26:21,144] [INFO] ===== Start GTDB Search =====
[2023-03-19 02:26:21,144] [INFO] Query marker FASTA already exists. Will reuse it. (OceanDNA-b14795/markers.fasta)
[2023-03-19 02:26:21,145] [INFO] Task started: Blastn
[2023-03-19 02:26:21,145] [INFO] Running command: blastn -query OceanDNA-b14795/markers.fasta -db /var/lib/cwl/stg4164167b-b57d-43ff-80b4-39941cdcd0c3/dqc_reference/reference_markers_gtdb.fasta -out OceanDNA-b14795/blast.markers.gtdb.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2023-03-19 02:26:22,084] [INFO] Task succeeded: Blastn
[2023-03-19 02:26:22,091] [INFO] Selected 15 target genomes.
[2023-03-19 02:26:22,091] [INFO] Target genome list was writen to OceanDNA-b14795/target_genomes_gtdb.txt
[2023-03-19 02:26:22,119] [INFO] Task started: fastANI
[2023-03-19 02:26:22,119] [INFO] Running command: fastANI --query /var/lib/cwl/stgfe68610f-8293-4d1a-a088-c1735caac03c/OceanDNA-b14795.fa --refList OceanDNA-b14795/target_genomes_gtdb.txt --output OceanDNA-b14795/fastani_result_gtdb.tsv --threads 1
[2023-03-19 02:26:25,233] [INFO] Task succeeded: fastANI
[2023-03-19 02:26:25,236] [INFO] Found 4 fastANI hits (0 hits with ANI > circumscription radius)
[2023-03-19 02:26:25,236] [INFO] GTDB search result
--------------------------------------------------------------------------------
accession	gtdb_species	ani	matched_fragments	total_fragments	gtdb_taxonomy	ani_circumscription_radius	mean_intra_species_ani	min_intra_species_ani	mean_intra_species_af	min_intra_species_af	num_clustered_genomes	status
GCA_002718455.1	s__GCA-2718455 sp002718455	91.639	393	426	d__Bacteria;p__Chloroflexota;c__Dehalococcoidia;o__UBA1151;f__TMED-70;g__GCA-2718455	95.0	N/A	N/A	N/A	N/A	1	-
GCA_002171675.1	s__TMED-70 sp002171675	77.0013	91	426	d__Bacteria;p__Chloroflexota;c__Dehalococcoidia;o__UBA1151;f__TMED-70;g__TMED-70	95.0	99.24	99.20	0.89	0.87	3	-
GCA_002719425.1	s__TMED-70 sp002719425	76.8508	78	426	d__Bacteria;p__Chloroflexota;c__Dehalococcoidia;o__UBA1151;f__TMED-70;g__TMED-70	95.0	N/A	N/A	N/A	N/A	1	-
GCA_008373205.1	s__TMED-70 sp008373205	76.805	112	426	d__Bacteria;p__Chloroflexota;c__Dehalococcoidia;o__UBA1151;f__TMED-70;g__TMED-70	95.0	99.62	99.62	0.87	0.87	2	-
--------------------------------------------------------------------------------
[2023-03-19 02:26:25,240] [INFO] GTDB search result was written to OceanDNA-b14795/result_gtdb.tsv
[2023-03-19 02:26:25,243] [INFO] ===== GTDB Search completed =====
[2023-03-19 02:26:25,247] [INFO] DFAST_QC result json was written to OceanDNA-b14795/dqc_result.json
[2023-03-19 02:26:25,247] [INFO] DFAST_QC completed!
[2023-03-19 02:26:25,247] [INFO] Total running time: 0h0m41s